In Footfall, the attackers have absolutely no idea about deceit and general dishonesty (although we, as a species, have raised it to a fine art). In Harry Turtledove's World War series, the invaders are just too inflexible so we run circles around them and steal their equipment. In Star Trek it is our solidarity and good nature that saves us from evil. In Babylon 5, we are the next coming - it being the dawn of the 3rd age of mankind an' all!

The oversights displayed by the seemingly clever alien species are incredible. The aliens in War of the Worlds only had to expose themselves to the world for them to be killed by a local virus! Again in Turtledove's books, the aliens never realised that in 1200 years,we would be able to go from sword swingings idiots to gun toting maniacs. A simple mistake really.

Whenever we get our hands on a new piece of kit, we somehow use it better than the invaders and beat the shit out of them! The only species that come close to our level of competancy are all less than 50 years ahead of us technologically. Case in point, V! Apart from their flying technology, nothing they had was particularly beyond our grasp.

Humans are the masters of beating the opposition at their own game, even when we should be incapable of playing (Dark City). We can out fly them, and slip in to their most heavily defended areas completely unharmed as in Independence Day, not forgetting that we have the ability to read leaked memories from mind controlling monsters!

Just for once, can't we have a foe that stands a chance of beating us. All these people being abducted is very melodramatic but when are we actually going to be in any danger?

Therefore since we have not actually been invaded yet, we have no personal, first-hand experience and must instead rely entirely on accounts we receive from such alternate realities.

Now that we have established our sources, we must consider them as reliable or unreliable, and also as a representative sample group or a non-representative sample group. Only if our sources are both reliable and representative of the whole can we make such absolute statements as "always" or "every" when considering our mortal enemies vís-a-vísfatal flaws.

Reliability

The question assumes that our sources are reliable, that is, that all alternate realties we have heard from are accurately representing the results of their alien invasions. We cannot ascertain the accuracy of these statements without evidence, but our only evidence is the statements themselves. But why would they lie? One possibility is that they are being forced to give false statements by the aliens who have, indeed, conquered them and wish to put us off our guard with false information. The reliability cannot be checked, and there is a possible motive for false information. Any stories we hear urging us to trade our nuclear missiles in for the alien's one weakness, delicious candy, should be viewed with suspicion. Therefore: the information cannot be regarded as reliable.

Representative Sample Group

This is the alternate Earth we assume when asking the question. These Earths have been invaded, discovered the invader's fatal flaw, exploited it, and survived. These Earths are likely giving us advance warning so we can identify the fatal flaws in our universe's analogous alien invaders.

Alternate Earths which have been invaded and were conquered:

Should an alternate Earth be invaded and conquered, we would likely hear nothing at all from them, or possibly even propaganda they were forced to deliver by their new alien overlords (see reliability, above). Much less likely, but still possible, are the warnings of a small but plucky group of freedom fighters which survives in isolated pockets of resistance, giving us advance warning before it is too late. This is the idea behind the Terminator series, although these mortal enemies of humanity are, in fact, terrestrial and beyond the scope of this article.

Conclusion

So we see that the stories we have heard of alien invasions are both unreliable and non-representative, and we cannot make such blanket statements as "alien mortal enemies of humanity always have some fatal flaw". Any stories of alternate Earths which have been invaded by mortal enemies of humanity without fatal flaws would be extremely unlikely to reach us, least of all with anything resembling reliable accuracy.

I personally really appreciated the alien race in Signs that had managed to travel millions of miles to get here, monitoring our planet for at least part of that journey and possibly before (let's take that planet F'Rahk-kul... No I need to pee, let's stop on the small green one there) but nonetheless never had picked up on the fact that two thirds of it's surface was covered with a material that was lethal to them.

Having typed this I do realise that less than a percent of our planet is actually water, and it is possible an alien race will view reality different from the way we do and they just never expected from their readings that that one percent would all be readily available to the inhabitants of the planet. Statistical likelihood of anyone on earth having water at all is very low, if you figure how few of the molecules around us is are actual watermolecules.

The same goes, to an extent, for the Footfall race, as you cannot plan or prepare for deception if you are incapable of imagining it. Humans will/might eventually be trying to conquer a distant planet and infallible as we imagine ourselves to be, and well planned as the attack will be, we will still be completely rebuffed almost effortlesslyby the inhabitants Sgh-lggl, which we didn't know about, can't explain and have no defense against.

The martians in the newish War of the Worlds, the Tom Cruise version, had been hiding out on our planet for yonks, though, so they were just stupid, which might also be a fair explanation for neglecting a fatal flaw, what with parsimonious thinking and all.

I think this is largely tied in with the fact that the only sample space we have is in fiction, which creates several reasons why the fatal flaws will occur:

We do not know what aliens are like. Given that we're not even sure if there is sentient lifeout there, predicting their methods, appearance, and of course weaknesses is so close to impossible as to be insignificant.

Fiction is written for entertainment. People will often prefer to read a story where man triumphs over the evil invaders from another planet, rather than a dismal tale of defeat by an invincible foe.

Human beings are flawed. We see flaws in ourselves and those we meet every day. Since sentient life is generally imagined to act
similarly to humans, they inherit things common to all of us, which includes our flaws.

So, in the end, the only real way of writing a completely realistic fiction involving aliens will be to actually come into contact with some. And, hopefully, it's only a matter of time...